Your part is mostly OK, except that nonconn1 is an ellipse rather than a circle (usually caused by removing a translate, but there may be other reasons as well). If you export the pcb as gerbers (file->export->for production-> extended gerber) and look at the gerber layers with a gerber viewer (I use gerbv) you will see one hole is producing a drill hole (it is in the drill layer) and the other (which is the ellipse) is not but rather is a copper pad. To fix that, select nonconn1 in the xml editor and change rx and ry to be the same value (I copied the r value from nonconn0 to both). That will make both nonconns holes as you intend. You may also want to copy the breadboard, icon and schematic files from the Sparkfun jack part so you new part has all three views (or if you just need the footprint leave as is). With the change to nonconn1 your part looks fine.
Peter